Sono called the current GBA scaling the *crispest* it can be but whether that is *best* is quite subjective.
I used some of sono's hints and the available tools to
hex edit some alternative GBA interpolation. Basically you can pick any middle ground you like between the default sharp but blocky/distorted and something soft/blurry but representing shapes better. You can also play around with sharpening too but I didn't find that to be worthwhile.
Sono said he was developing patches for GBA in parallel with DS. His widescreen patcher even has a hidden mode that does it for GBA too. I don't know if this new approach using 3DS communication is going to change those plans.